Gueye spent his early career in Senegal for Diambars before joining French club Lille in 2008. He broke through into the first team in the 2010–11 season, in which Lille won Ligue 1, and became a regular starter in the league and the UEFA Champions League over the following four seasons.
Aston Villa paid Lille £9m for the service of Idrissa, fighting off interest from Southampton, and he signed for the club on 10 July 2015 On 8 August 2015, he made his debut in a 1–0 away victory over AFC Bournemouth. On 19 January 2016, Gueye made his first and only goal for Villa in a 2–0 over Wycombe Wanderers in the third round replay of the FA Cup.
In total he made 35 league appearances for Villa in the season where they were relegated from the Premier League.
Gueye made his international debut for Senegal in 2011, and has appeared in FIFA World Cup qualifying matches for them. He also represented them at the 2012 Olympics, at the 2015 Africa Cup of Nations and at the 2017 Africa Cup of Nations.